Differential expression analysis after RUVseq in Galaxy
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14 months ago
tanya_fiskur ▴ 40

Hello everyone.

Guys, how can I use the tables, produced by the Galaxy-embedded RUVseq? Its output looks like this:

batch_effects_control_method_k1    

identifier  condition   W_1
Counts_s1.tabular   Cont    -0.343905680583747
Counts_s2.tabular   Cont    0.581535965604329
Counts_s3.tabular   Cont    -0.285812794268053
Counts_s4.tabular   Treat   -0.25027199487464
Counts_s5.tabular   Treat   -0.271891634519469
Counts_s6.tabular   Treat   0.570346138641578

... and similar tables for the "batch_effects_replicate_method_k1" and "batch_effects_replicate_method_k1".

How can I use these tables for differential expression analysis, ideally, in the Galaxy itself?

(I tried to run RUVseq in the R-studio too, as it is written in the tutorial (http://bioconductor.org/packages/release/bioc/vignettes/RUVSeq/inst/doc/RUVSeq.pdf), but, for some reason, it didn't work).

Thanks in advance for any help.

Galaxy RNA-Seq RUVseq EdgeR Limma-voom • 371 views
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